Biology subjects

Bantignies, F.

Publications and source records attributed to Bantignies, F..

6 recordsLinked to original sources

bioRxiv2026

Genome expansions and regulatory contact entanglement help preserve ancestral metazoan synteny

Chromosomes constitute deeply conserved evolutionary units in many metazoan genomes, with chromosomal fusions and fissions, accompanied by sub-chromosomal rearrangements, rewiring three dimensional genome architecture. How chromatin loops and compartments that define distal regulatory interactions within chromosomes impose functional constraints that affect this long-term evolutionary process (and vice-versa) is an emerging research topic. Genome expansions, especially through transposable element (TE) activity, test these constraints by increasing the genomic distances over which regulatory interactions must function and were thus suggested to be the drivers of chromosomal rearrangements. To study dynamics and stability of such distal interactions in the light of genome expansions, we focus on the cnidarian Hydra vulgaris, which, based on its simple and well-understood biology as well as one of the largest genomes among cnidarians, is particularly suited to test how chromatin loop and genome architecture respond to genome expansion. We investigate genome architecture using Micro-C, single-cell Hi-C (Dip-C), and DNA FISH, and perform comparative analysis using available genomic and epigenomic data. Contrary to prior expectations, our analysis of whole-genome data and particular loci (e.g., Wnt) suggests a scenario where genome expansion did not only result in chromatin loops often reaching several megabases in hydra, but also led to regulatory contact mixing and entanglement, introducing additional constraints to maintain ancestral genomic architecture. Generalizing these findings across hundreds of metazoan genomes, we show a new mechanistic role for genome expansion in yielding entangled long-range regulatory configurations that, in turn, decelerate chromosomal rearrangements, thus maintaining (and not breaking) ancestral regulatory states and synteny. Significance statementSome of the largest and most repetitive animal genomes retain a surprisingly high level of deeply conserved metazoan synteny. As repetitive regions are often associated with chromosomal rearrangements, it has been enigmatic why syntenic retention is so frequently observed. In this study, using hydra as a model system for both stem cell biology and an evolutionary history rich in transposable-element driven genome expansion, a multi-level conformational landscape dissection reveals a multitude of long-range regulatory states. We show that mixing of multiple such regulatory links accompanied by genomic expansion is associated with maintained ancestral synteny, thus pointing to the counter-intuitive role of genome expansions as "fossilization" agents across metazoan genomes.

evolutionary biology↗

bioRxiv2024

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

1Upon differentiation chromatin rewires to reflect its new cellular identity and function. While it is widely known that this process involves cooperative changes in transcription, chromatin composition and 3D conformation, it is unclear what exactly drives these changes and how they influence one another. Here we used ESC-to-NPC differentiation to study rewiring at a 3 Mb large neuronal Zfp608 locus. During this process, this large chromatin domain splits in half right at the Zfp608 promoter, local chromatin gets littered with activating marks, compacts in 3D space and Zfp608 abounds in transcription. We investigated the cis and trans elements using capture Hi-C (cHi-C), extensive biophysical modelling, and 3-colour 3D-FISH with technical and analytical breakthroughs and found that transcription abundance modulates the contacts in the region as well as the insulation at the domain split. Furthermore, we found a genetic element we named scaffolding element, with a dual enhancer and architectural function that is essential for chromatin rewiring and loop formation at the NPC stage. The loss of this element disrupts the formation of all local NPC-loops irrespective if they are anchored in this element or not, highlighting the hierarchical relationship between elements that act as loop anchors. Furthermore, we uncovered that the scaffolding function, although driven by multiple mechanisms, can form loops independent of loop-extrusion and that other molecular attractions were necessary to form NPC-specific contacts in the region. Together, these results demonstrate that a hierarchy of genetic elements in cis allows successful rewiring during differentiation and that multiple trans acting elements contribute to make this rewiring efficient.

cell biology↗

bioRxiv2023

Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila

Non-genetic information can be inherited across generations by the process of Transgenerational Epigenetic Inheritance (TEI). TEI can be established by various triggering events, including transient genetic perturbations. In Drosophila, hemizygosity of the Fab-7 regulatory element triggers inheritance of the histone mark H3K27me3 at a homologous locus on another chromosome, resulting in heritable epigenetic differences in eye colour. By mutating transcription factor binding sites within the Fab-7 element, we demonstrate the importance of two proteins in the establishment and maintenance of TEI: GAGA-factor and Pleiohomeotic. We show that these proteins function by recruiting the Polycomb Repressive Complex 2 and by mediating interchromosomal chromatin contacts between Fab-7 and its homologous locus. Finally, using an in vivo synthetic biology system to induce them, we show that chromatin contacts alone can establish TEI, providing a mechanism by which hemizygosity of one locus can establish epigenetic memory at another in trans through long-distance chromatin contacts.

genetics↗

bioRxiv2022

Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes

Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. Here, we used multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development. Notably, 3D proximity between Pc targets is rare and involves predominantly pairwise interactions. These 3D proximities are particularly enhanced in segments where Pc genes are co-repressed. In addition, segment-specific expression of Hox Pc targets leads to their spatial segregation from Pc repressed genes. Finally, non-Hox Pc targets are proximal in regions where they are co-expressed. These results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not involve clustering of multiple distant Pc genes.

genetics↗

bioRxiv2021

Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs

Cohesin loop extrusion facilitates precise gene expression by continuously driving promoters to sample all enhancers located within the same topologically-associated domain (TAD). However, many TADs contain multiple genes with divergent expression patterns, thereby indicating additional forces further refine how enhancer activities are utilised. Here, we unravel the mechanisms enabling a new gene, Rex1, to emerge with divergent expression within the ancient Fat1 TAD in placental mammals. We show that such divergent expression is not determined by a strict enhancer-promoter compatibility code, intra-TAD position or nuclear envelope-attachment. Instead, TAD-restructuring in embryonic stem cells (ESCs) separates Rex1 and Fat1 with distinct proximal enhancers that independently drive their expression. By contrast, in later embryonic tissues, DNA methylation renders the inactive Rex1 promoter profoundly unresponsive to Fat1 enhancers within the intact TAD. Combined, these features adapted an ancient regulatory landscape during evolution to support two entirely independent Rex1 and Fat1 expression programs. Thus, rather than operating only as rigid blocks of co-regulated genes, TAD-regulatory landscapes can orchestrate complex divergent expression patterns in evolution. HIGHLIGHTSO_LINew genes can emerge in evolution without taking on the expression pattern of their surrounding pre-existing TAD. C_LIO_LICompartmentalisation can restructure seemingly evolutionarily stable TADs to control a promoters access to enhancers. C_LIO_LILamina-associated domains neither prevent transcriptional activation nor enhancer-promoter communication. C_LIO_LIRepression rather than promoter-specificity refines when genes respond to promiscuous enhancer activities in specific tissues. C_LI

genetics↗

bioRxiv2017

Single-cell absolute contact probability detection reveals that chromosomes are organized by modulated stochasticity

At the kilo- to mega-base pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combined high-content super-resolution microscopies with state-of-the-art DNA labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We found that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we were able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs were to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.

biophysics↗